chr5-35026465-G-GT
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_031900.4(AGXT2):c.814_815insA(p.Thr272AsnfsTer37) variant causes a frameshift change. The variant allele was found at a frequency of 0.00000479 in 1,461,556 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000048 ( 0 hom. )
Consequence
AGXT2
NM_031900.4 frameshift
NM_031900.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.98
Genes affected
AGXT2 (HGNC:14412): (alanine--glyoxylate aminotransferase 2) The protein encoded by this gene is a class III pyridoxal-phosphate-dependent mitochondrial aminotransferase. It catalyzes the conversion of glyoxylate to glycine using L-alanine as the amino donor. It is an important regulator of methylarginines and is involved in the control of blood pressure in kidney. Polymorphisms in this gene affect methylarginine and beta-aminoisobutyrate metabolism, and are associated with carotid atherosclerosis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| AGXT2 | NM_031900.4 | c.814_815insA | p.Thr272AsnfsTer37 | frameshift_variant | 8/14 | ENST00000231420.11 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| AGXT2 | ENST00000231420.11 | c.814_815insA | p.Thr272AsnfsTer37 | frameshift_variant | 8/14 | 1 | NM_031900.4 | P1 | |
| AGXT2 | ENST00000510428.1 | c.814_815insA | p.Thr272AsnfsTer37 | frameshift_variant | 8/13 | 1 | |||
| AGXT2 | ENST00000618015.4 | c.814_815insA | p.Thr272AsnfsTer37 | frameshift_variant | 8/12 | 5 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251144Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135752
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GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461556Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727082
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GnomAD4 genome
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Beta-aminoisobutyric acid, urinary excretion of Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center | Apr 04, 2024 | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at